The Clone
by jCOOLn
Summary: Harry's life is an illusion created by Mastermind at the request of Sinister. Harry is a male clone of Rogue created by Sinister to kill Cassandra Nova after he learns of her plan to wipe out all mutants. Harry does kill Cassandra with his powers, but then turns on Sinister. Now he is alone in a world he barely understands. Harem/Mutant/Super-Genius/OC/Lemons


**Title: The Clone**

 **Chapter One: Just a Clone**

 **Disclaimer: I don't own Harry Potter, nor do I own Marvel/X-Men, so don't sue me**

 **-I am a free writer, and I write when I feel like it, I am not on a schedule, so therefore updates will be infrequent.**

 **-If I lose interest in this story I might just stop writing all together, though in the future I may find interest in it again and then take up updating it then.**

 **-There may be lemons, profane language, character/death, prostitution, possibly torture or abuse (though not on Harry), lying, and probably other sins. If this bothers, you then don't read. You have been warned.**

 **-Harry may participate in polygamy/bigamy, extramarital relations, and other acts of sexuality, though no homosexuality, so if this bothers you then don't read.**

 **XXX**

Just as the green light hit him Harry's eyes opened. Instead of being dead or even in a forest his surroundings were shocking. It took his brain a moment to accept the sudden change in surroundings. Instead of the darkness of the Dark Forest he was floating in some sort of tube. A breather had been placed over his face so he could breathe while needles pierced his flesh in various places. What they were doing he could not guess. Maybe taking fluids from him, pumping chemicals in, or perhaps they were just there as monitoring equipment.

He tried to move yet found his body to be sluggish. He stopped trying relatively quickly. His eyes which were squinted thanks to the liquid peered out. The liquid was green and as such everything he saw had such a tint to it. After a moment his vision cleared up. He realized quickly that he was in a lab. Scientific equipment he had never seen before ran the length of the apparently rectangular room. After a moment he counted five people. Two of them were females while the other three were men. He knew they were scientists due to the white lab coats they wore. It gave them a cold clinical feel.

His heart started to race. He had no clue as to why he was there. For that matter he couldn't figure out how he had gotten there. The worst case scenario was government agents had kidnapped him and were planning on experimenting on him. If that were the case then he feared greatly. Not only for his own sake, but for what such actions would cause. Worst case scenario a war between the magical communities and the muggle ones would start up. Such bloodshed would be fought for such petty reasons.

A scientist off to the right looked down at the machine before turning his way. As their eyes met he seemed startled. Harry watched as the heavyset man scurried over to an intercom system and pushed the button. Harry couldn't read lip, so he had no clue what the man was saying, yet whatever was spoken was done so frantically. At this point all of the scientists were looking at him. It didn't do him any favors. He felt like some sort of lab animal.

Then all of a sudden a chemical was pumped into his system. The woman closest to him had done something by the looks of it. He wasn't getting sleepy, just calm. His mind started to feel as if it had been filled with fuzzy static. It was nice in all honesty. It also helped as the person who walked into the room would have caused his hairs to stand on end had he not been so calmed.

He was a tall man by Harry's reckoning. He stood over the tallest scientist by at least a foot. His sin was unnaturally white. It was like milk glass in appearance. On his forehead was a strange diamond symbol the color of crimson red. His hair was slicked back like a nineteen eighties gangster and as black as the night. Compared to a normal man he was extremely muscular. His muscles bulged like some guy who spent all his time in the gym. And the clothes he wore were an oddity. It was like some sort of armor with a double colored cape. The back was a dark blue while the interior was a bright red. All in all the man was extremely odd looking.

Another positive side effect of the drugs they had given him was an amazing poker face. Had Harry been in the right state of mind then he would have been able to appreciate this. As it stood he seemed just a moronic sack of skin and bones floating in green fluids. Even the spark of curiosity in his eyes seemed dim to the casual observer.

Mister Sinister looked at the clone floating in a jar of preservative fluids with cold eyes. It was a product to him, nothing more. He turned to the scientist in his employ and began asking them about certain variables regarding his creation. They confirmed that he awoke no less than five minutes ago. It was good. He didn't want such a dangerous creation to have any opportunity of escaping. While confident in his ability to control him he did not like to take risks.

His colleague followed him through the door. The unassuming man was Mastermind, a mutant criminal he had employed in this venture. His ability to cast realistic illusions with his mind were needed if they were to counter Cassandra's powers. While he would have preferred a mindless puppet Cassandra would have simply possessed it. If that were to happen then they would be in for a dangerous battle. Therefore the clone needed a strong will of its own. For this reason he had taken steps to ensure his loyalty until time for his extermination.

"Did the illusions work?" Mastermind glanced at Sinister before gazing at the floating boy.

"Yes, but I warn you, his past doesn't have any real combat training. He's just a normal boy who thinks he can use magic. He won't be much of an asset against her." Sinister nodded his head.

"You and I will be enough to subdue her. He is only needed to destroy her as to prevent her from possessing someone else. Once her astral form has been destroyed I will activate the cellular breakdown failsafe placed in his DNA. With that we will be able to wash our hands of this mess." Mastermind nodded his head acknowledging his plan.

"And the Sentinels? What will we do about them?" There was a pause.

"Destroy them." Mastermind raised an eyebrow. "They were built to kill mutants, so they have no purpose for me."

Sinister walked forward to continue talking with the scientists. Mastermind nodded his head. "As you wish."

Dr. Ophelia stepped forward and handed Sinister a datasheet. "The vitals are fine, his brainwaves are normal, and his genetic structure is holding together perfectly."

"What is this spike in heartrate?" She took the paper back and looked it over.

"His death." She indicated to Mastermind. "After his _development_ was complete his life was ended. This brought him into consciousness and was used to awaken his mutant powers."

"So his powers are confirmed?" She shook her head no.

"No, we have not been able to test that yet. We suspect that they have, but until an actual test can be conducted we will not be sure." Sinister accepted this.

Mastermind stepped forward. "We cannot test his powers on someone else. He will gain their memories and from them an understanding of what is going on."

Sinister casually agreed. "From my own understanding these markers here indicate that his mutant power should be active." He pulled out a bottle of pills. "And if it is not we can always use this. It will forcefully awaken his X-Gene, and since he is disposable the damage is acceptable."

"When can he be moved?" Dr. Ophelia turned to Mastermind.

"As soon as you need him to be." Mastermind grinned, happy things were moving so smoothly.

Sinister put the notes down. "Prepare the jet, load the subject, and get started on the next project." Everyone acknowledged his orders and got to work.

Harry watched the scientists scurrying around like rodents trying to do whatever it was the two weird people were telling them to. Instinctively he didn't make eye contact with either of the newcomers. Whatever they were planning allowing them into his head probably wasn't wise. That and he didn't want them to take too much of a direct interest in him.

Had he not been pumped full of drugs a sigh of relief would have left him as the two men left the room. Regardless, his five friends were not much for social conversation. Even through the drugs he did feel a bit insulted as they draped a cloth over his tube like he was some sort of parrot that would fall asleep or something. Granted he did soon fall back asleep, but he attributed that more to getting another round of drugs as opposed to the cloth.

The next thing Harry knew he was being jerked around. Even through the liquid he was still floating in he could recognize the sound of a jet engine in the background. As the engine began to whine a little less he instinctively braced himself. A sudden jerk soon came, but the fluid prevent too much of a shift. It became apparent to Harry that the plane he was in just landed. Where he was no he had no clue.

Fifteen minutes later the back hatch of the plane opened up and strong men began to wheel his tube outside. He had to squint as the sun hung high in the sky bright as he had ever seen it. While his eyes were closed a beeping sound started to echo through the water. As he looked down he saw the diamond marked man pressing some buttons at the base. When he pushed a final one the glass opened almost like a flower and the fluids rushed out.

Harry fell lifelessly onto his face as gravity once again exerted its control over him. Some of the scientists who had been in the room with him when he woke up for the first time were there once again. They stepped forward and began pulled the needles out of his skin. It stung a bit, but not too bad. It was the removal of the oxygen mask that really woke him up. A hot dry air soon filled his lungs causing him to start coughing for a moment.

"Are you sure this is going to work?" A deep voice behind him asked in a questioning tone. As Harry looked back he saw the shorter one looking up at the diamond marked man with questioning eyes.

"He will do" was all the tall one said.

The scientists gave him clothes that resembled those of a patient. As he put them on he felt how weak his muscles were. He began to question just how long he had been in that tube. That of course was secondary to what they had in mind for him at that moment. He made sure to take his time so that he could get a good lay of the land. It wasn't promising.

In every direction he looked there was jungle. If that wasn't bad the type of woods was not one he recognized. These trees were far more tropical than the ones he was used to. The bugs flying around them all, the blazing sun, dry air, and a myriad of other little things made him start to believe they were much closer to the equator than he had ever been in his life. What country that meant he was in now he couldn't say. What was more worrying than anything was that no one had come to save him yet.

"Are you done sightseeing?" Harry turned his head to look at the diamond marked man. "I can see that you have many questions, but unfortunately we are on a tight schedule. If you want to figure out what is going on then I suggest you do everything that your told."

Harry definitely didn't like that, but nodded his head anyways. "Good." The man pulled out a pair of white gloves before tossing them to Harry. "First, put those gloves on. You are not to remove them under any circumstances unless I give you specific directions."

Complying, Harry put on the gloves which fit him quite comfortably. "Now, you are to follow us. You may not talk. This mission requite the utmost secrecy." Again he nodded his head. "I will tell you this. My name is Nathaniel Essex, and this is my colleague Jason Wyngarde. You may refer to me as Mister Sinister, and him as Mastermind. Are we clear?" The boy nodded his head. "Good, you learn fast. Should you do a good enough job all of your questions will be answered."

From there Harry followed the two men to a military jeep. He was made to sit in the back while the two men sat in the front. Off to the side Harry noticed other strange looking people. He counted five of them in total. They occupied a second military jeep that drove off in front of them.

As they road down the narrow dirt path Harry took note of his surroundings. The two men who had introduced themselves to him looked quite relaxed. This indicated to Harry that they were used to being in control and were quite powerful. The ones in front were slightly tense, yet in a savage way. He rated them as soldiers of some sort. Probably bodyguards or elite paramilitary soldiers. Whatever they were going to do it was not friendly. Harry only hoped he could run away when things went to hell.

As the road continued to wind he took note of his surroundings. Large canopy leave that were perpetually covered in rainwater was clearly abundant. The mud puddles they frequently passed seemed recent. The colorful birds and occasional monkey they passed by stared at them oddly. It became apparent to Harry that he must be in South America or some other tropical country. An island nation was possible, but he couldn't be sure.

Why he had been dragged all the way out to South America he could not even begin to fathom. On the one hand he was grateful to not be a test subject subjugated to all sorts of inhumane tests, but the anticipation of what they were doing was eating away at him. He once caught the green haired woman looking at him, before grinning. That grin was not sweet. It had a twisted sadistic tinge to it. It was like she could watch someone die and not even blink. It reminded him all too much about the way a certain someone treated others.

After hours in the jeep they came to a stop. The savage looking blond man hopped out. Although he was a distance away Harry could have sworn he was sniffing the air like some sort of dog. After that he came up to their jeep and told Mister Sinister the base's location. Surprisingly Mister Sinister took this at face value. All Harry could think of was the word, base.

A million questions and theories seemed to run through his head after that. He was getting worried that these people were going to get him mixed up in some international incident.

"Get out of the jeep and stick close to me." Mister Sinister broke him out of his train of thought. Harry complied and crawled out of the jeep. "You will need to be a silent as possible." With that they began walking through the dense jungle.

More than once Harry's foot got stuck in a mud hole, or he ran into a giant spider web, yet never did he fall too far behind Mister Sinister and his group. Partially out of fear as to what they would do to him, and partially out of necessity. Harry knew he would not be able to survive in the jungle for long without magic. At the moment these dangerous people were his only life line.

After what felt like an eternity they came to the forest's edge. They all were hidden so well that Harry felt he stuck out like a Christmas light. The sun was just starting to set, so Harry could still see the base with clarity.

A barbwire fence surrounded the entire thing. The other wires braided into its length made him suspect it was electric. Behind the fence was a large stretch of cleared space. At each corner of the stone base were high guard towers where snipers would be able to clearly take out anyone who got past the fence. Then there was the base itself. It was made from solid concrete, yet it was quite small. Harry assumed that most of it would be underground.

The team that had been brought with them were whispering amongst themselves. Mister Sinister and Mastermind seemed to watch with some form of amusement. Then the bald one with tattoos suddenly grabbed a hold of two of them before disappearing. In an instant he was back without the other two and grabbed the other two members of their team. After that Sinister and Mastermind stood up and walked out of the woods with Harry hot on their heels.

He grew nervous as they got closer to the gate, but then it opened up. The two leaders did not seem surprised and just casually kept walking. Harry kept looking at the two closest watch towers expecting to get shot at any moment, yet as they came to the front door not one shot was fire.

They came to a stop in front of a massive metal door tall enough even for Sinister to walk under without issue. After a moment it opened up. On the other side was the bald tattooed guy standing there with the rest of the team. The casualness of it all was a bit overwhelming.

"Any alarms?"

The feral looking man shook his head. "No, but she still knows where here, right?"

Sinister nodded his head. "Yes, I suspect she does."

Nothing else was said as the five soldiers went out ahead of them. The ability to teleport was a magical one, so Harry suspected that the rest of them could use magic, and were therefore probably international magical terrorists of some kind. The only flaw in this theory was the scientists, and what they needed him for. Magic users did not do science and he didn't think his skills were anything that these men couldn't pull off on their own. As such he wondered what part he was supposed to play.

As they moved down the stairwell Harry tried to block the sounds of fighting. The occasional dead body on the floor was also quite unpleasant. Some were killed humanely while others seemed to have been savaged by a wild bear. On occasion there was a gunshot and despite himself Harry hoped that those muggle weapons killed at least one of his captors. Yet as they made their way to the bottom all eight of them were still in one piece.

Mister Sinister stopped and turned back to look at him. "Take off your gloves." Confused, but obedient, Harry did as he was told. "Now, make sure that you do not touch anyone, but the woman in this room. I will tell when to do it. Do you understand?" The force of his tone made Harry take a step back.

"Yes, Mister Sinister." The man grinned.

"Good, now stick close to me." With that the final door to the base of the complex was opened.

Harry gaped in amazement by what he saw. The bunker was far larger than he had ever suspected. It was so large in fact that he could not see the end of it. Yet that was not the only thing that shocked him. Standing shoulder to shoulder were dozens of massive robot at least thirty feet tall each. While they looked a little basic it still amazed him that something like this was possible. He would have continued to gape at the robots had a voice not called out to them from a distance.

"So you have finally come." The female tone was high and thin. "Though I never suspected you of all people would come. My, my, my, how you have surprised me."

The woman standing off in the distance surprised Harry. Whatever he had been expecting it was not a bald older woman wearing a Panama Jack outfit. She seemed harmless on her own. Yet, it was that look in her eyes that sent chills down Harry's spine. The cold confidence she extruded even ganged up like that was not false. She knew something they didn't. Whatever it was Harry didn't want to find out.

"Normally I would have washed my hands of such matters, but." Sinister took a moment to glare at her. She just smirked in return. "You are getting in the way of my research. That is not something I can permit."

She shrugged her shoulders. "I am only doing a bit of vermin control. What is so wrong with that?"

For the first time since meeting him, Harry saw Sinister angry. It was not a look he liked. "You are trying to stop evolution. That is a crime that cannot be forgiven."

"You call these freaks evolution do you?" The word freak caused Harry to flinch though no one noticed. "My, what a deranged man you are." Her grin spread though it did not make her anymore charming. At the end of it her face looked like someone stretched a peace of latex across a skull. "Then again I can see you have infected yourself with their DNA, so how could I have expected anymore from you?"

In a flash one of the soldiers grabbed a throwing javelin of some sorts and threw it at her. To Harry's shock the javelin seemed to turn into a glowing arc of energy. Just as it was about to hit her however a barrier formed around her. An explosion that shredded all the nearby metal soon sounded, yet when the dust cleared she still stood there perfectly fine.

A piece of metal that had been torn from the wall rolled up to create a makeshift javelin. With incredible speed she somehow sent it flying right back at the man. Before the rolled up scrap metal could turn the man into a shish kabob a whirlwind of air formed around him. The air currents were so powerful that it redirected the metal javelin into a nearby wall where it embedded itself.

"You have quite the team there Essex." The Panama Jack wearing woman smiled. "But you cannot truly believe them capable of taking someone like me on."

"Miss Cassandra, I can assure you that after today, you will be dead and gone." With that they all attacked her at once.

The battle was fierce. Pieces of metal were being hurled all over the place. Blasts of energy from various people bounced off of the old woman's shield. The feral man tried to strike her from the back only to be pushed through the metal sheet wall. Cassandra tried to take them out, but they worked as a team. When one was about to be taken out another would protect them. They also did well offensively combining long range with short range attacks.

As the battle dragged on the team started to get the upper hand. Essex had not gotten involved. He seemed to be saving his energy for something. Harry had also been kept in reserves, not that he would have been able to do much in a battle like this absent his wand. It was baffling to him how these people were able to do these things without wands. Even with wands some of the stuff they did didn't seem plausible.

Eventually Cassaundra pushed them all back and prepared for something big. Whatever it was she was planning on was stopped as the feral man that got pushed into the wall, who Harry was sure was down and out, attacked her from the back. She didn't have time to put up her shield this time and took his attack directly. The mauling was intense as bits and pieces of her flesh were ripped from her bones. In an instant she was missing a third of her body mass.

Essex stepped forward staring down smugly at the dying woman. Still, even this far beaten, she remained confident.

"You think you have won, don't you?" She shook her head as if he was the one about to die.

"You are beaten Cassandra, don't demean your defeat." He went to gesture for Harry only to stop.

"You thought it was eight against one? No, it has been dozens against eight." With that she activated a device on her wrist. At first nothing happened, but then the giant robots began to move. "Goodbye, Mister Sinister."

Essex looked to the side just in time for a massive metal fist to nearly crush him. He unleashed a blast of energy from his hand that tore a hole in the machine's chest. It went down quickly, but two more soon took its place.

"Boy, do it now!" Sinister looked at him as he fought off several giant metal robots.

Harry was startled. The giant machines were just about to kill them and this guy still wanted him to touch this creepy old lady? He had no clue why, but felt that if he was going to survive he would need to trust this guy, as much as it was safe to do so.

He rushed over to the old lady who only got a moment to look at him before his hands touched her. In an instant he wished he hadn't. It was like he was eating her. Every bite was like taking a piece of her into him. Memories flashed across him mind that were not his own. Energy pulsed through his body in ways it never had before. And this otherness seemed to fill him. He fought it as best he could yet no matter what he did a piece still remained. At the end of it the presence was crushed and his body feasted on the remains.

The Marauders, Sinister, and Mastermind breathed a sigh of relief as the Sentinels stopped attacking them. When they looked back and saw the unconscious Harry Potter next to a pile of dust that was once Cassandra Nova they realized the plan had worked. Essex landed next to Harry and began to examine him. No doubt he would want to research the corpse once he returned to his lab.

"Is he still alive?" Mastermind walked up behind Sinister. He had taken a few hits during the fight. His illusionary abilities were severely limited against pure machines after all.

"Yes, he is simply unconscious. The memories were perhaps too much for his mind to handle." His finger pealed back the eyelashes to reveal a dull lightless eye.

"Are you going to exterminate him now?" Sinister paused for a moment.

"No, I will bring him back to my lab. I would like to see if his genetics have changed from absorbing Cassandra."

Mastermind nodded his head having expected as such. "Very well, but first we need to deal with these Sentinels."

Sinister forced himself away from examining Harry's body. "Of course. We need to be quick or else his cells will begin to breakdown however."

After that the Marauders began to absolutely wreck the remaining sentinels. It took several hours, but eventually there was nothing but scraps. Even then Essex wanted to be thorough, so he planted an explosive device at the center of the complex more than powerful enough to destroy it and everything around it with no chance of anything ever being recovered again. When everything was said and done they all began to return to the jeeps.

Nathaniel stayed back to collect Harry's body. As he returned to the basement he saw the boy still lying in the same exact position. He flipped him over no longer able to hold back his curiosity. While examining his skin he noticed something odd. The elasticity had not begun to weaken. The boy was technically supposed to last twenty four hours after being released from his tube, but still at this point there should be at least some deterioration.

"What is going on?" As he was thinking he did not take notice that Harry's eyes were no longer dull.

"Cassandra Nova had a healing factor." Essex looked down at the perfectly lucid Harry glaring up at him. Before he could do anything Harry had grabbed him by the ankle. "That healing factor has been countering your little genetic failsafe since I absorbed her."

Nathaniel gasped feeling all of his life energies being drained away. He gritted his teeth glaring down at the boy as he tried to break away. "Release me this instant boy!"

Harry just glared back at the man ignoring as best he could the horrors flashing across his mind. "No." This man was much older than he had anticipated. "You are a monster, and I cannot let one such as you continue living."

Sinister tried to call for help, but nothing came out. His skin began to sink in on itself, his strength had already been reduced considerably, and none of his powers were working. As he fell next to Harry looking into those hate filled eyes all he could say was, "I created you."

The last things he would ever hear was one of his creations replying, "And I killed you" before the last of his life-force was pulled out. In an instant Nathaniel's body was reduced to dust just as Cassandra's had been. Their ash piles left next to one another for all time in a strange twist of irony.

Harry just relaxed. He didn't try to rationalize the horrid memories of over a hundred years of torturous experimentations flashing through his mind. The damage done by Cassandra's memories alone were enough to leave him emotional worn out? Only the knowledge that Essex would come back if he didn't do something made him move. He would have been happy to let the bomb destroy him, but he would not allow Essex to come back. He would make it his life goal to destroy him permanently if need be.

With that Harry accessed one of the mutant powers Essex had spliced into his genes before his death. Without making a sound Harry teleported himself away from the complex.

His colleagues would wonder where Essex had gone to, but not for long. They were allies in a single cause, not friends. When the explosion went off they would just assume he went off on his own to do his own thing. None would realize the truth until much later.


End file.
